Salmon Confidential, a fish out of water

In early March of this year, documentarian Twyla Roscovich released a feature film titled Salmon Confidential. The documentary takes a polemic approach to salmon farming in British Columbia. I first learned of the documentary when an article popped up in a Google news feed I have set up for aquatic animal health. In that article, Twyla was responding to some commentators including those working for fish farming companies. She mentioned the science background that props up her documentary, so I decided to watch it for myself.

This review will follow the science of fish health in the documentary chronologically, and I'll finish with some more high level discussion points that I think run through the debate between the activists and the farm supporters. The film features edited content from many familiar names in the debate: Alexandra Morton, Dr. Rick Routledge, Dr. Gary Marty, Dr. Kristi Miller, Dr. Fred Kibenge, and many others. I won't really comment on the filmography of the piece, though obviously that contributes to the flavour one might take from the film.

The film jumps into the pool prefacing with the decline of the Fraser River sockeye. It's generally well known that productivity has been falling in the Fraser River. But what is not well known, is that the decline is not equal amongst all the stocks in the Fraser River. For example, Harrison Riversockeye salmon have shown increasing escapement since 2008. The Harrison River stock differs from the rest of the Fraser River sockeye, in that they spend a very short period in freshwater. They migrate towards the marine environment after emerging from the gravel spawning beds. Some migrate North through the Strait of Georgia, while others migrate west through the Juan de Fuca Strait. Those travelling west winter off the West Coast of Vancouver Island, where there are more than 30 farm leases. For those heading up through the Campbell River area, there are even more farms. If the farms are causing mortality when the salmon swim past, how is it that this stock is increasing? Indeed, heading to sea early would make them more susceptible to the salmon lice that Alexandra Morton showed pictures of. Later in the documentary Morton refers to the Harrison River stock, and claims they never swim past salmon farms. That is simply untrue. As you'll see more of, they never say where the data comes from when she shows the "migration route", and it clearly conflicts with the Harrison River stock data I've linked to above. Another bit of inconvenient science for the film narrative is that similar declines in overall productivity have been documented in Alaska, where aquaculture is outlawed (sort of, more on that later), and also in Oregon. In fact, there are similar productivity declines throughout the salmon of the Pacific, from California, all the way up to Alaska. That is a clear picture of something larger, when the trend shows up significantly across a very large geographic region, and coincidentally in time.

Moving on, the film begins to talk about the pre-spawn mortality in the rivers. Again, this differs by stock, and one of the variables that the Cohen Commission discussed was climate change.The rivers have warmed by about 0.7°C, and this had an uneven impact on the spawning populations. There is evidence, as with the Harrison River juveniles, that timing is the crucial factor. The summer runs tended to have lower losses than the early and late season runs. Clearly there are stock specific coping abilities when it comes to the increased temperature. So, what Morton calls an epidemic is not really so. Further, Roscovich makes no mention of other factors, a common theme throughout the film. A recent study for example has linked highway runoff to pre-spawn mortality. The lack of context is habitual throughout the film. Worse, in some cases, current and relevant data is ignored:

First, it's not at all clear where the data comes from. If it is all stocks of sockeye, all Fraser River sockeye, all Fraser River salmon, or even all Pacific salmon. But the most devious part of this graph is that it stops at 2009. This film was just released, so one would assume they had access to data from 2012 at least, and when that is included, things look very different:
Quite different. This image comes from the 2012 DFO pre-season forecasts for Fraser River Sockeye. The first thing to jump out is that huge record return in 2010. The second, is that the productivity appears to be coming back to long-term average, though the year to year variability is now much higher than earlier in the time series.

One of the favourite topics for Morton and her colleagues used to be sea lice. Following the productivity topic above, the film cuts to Morton showing some Pacific salmon smolts carrying sea lice. Morton makes the erroneous claim that sea lice are not naturally carried by Pacific salmon. This is false. The Pacific salmon tend to be more naturally resistant to the sea lice, but they do carry them. The sea lice does not survive in freshwater, so they could not have made their way into the Pacific Ocean on hatchery raised Atlantic salmon. In fact, scientific research has shown that there are genetic differences that suggest independent evolution of Lepeophtheirus salmonis between the Pacific and Atlantic varieties. What's more, recent long term research from Ireland has shown that sea lice infestation is unlikely to be a significant cause of mortality. The research there released smolts in Irish rivers over a period of nearly ten years, and split them between two groups. One receiving a sea lice treatment before release, the other would receive no treatment. Then they count the returning adults. In the end, the differences were tiny, 5.6% of the treated group returned, while 4.8% of the control group returned.

From this, the film jumps into viruses. We are introduced to research from Dr. Kristi Miller, a DFO scientist. Dr. Miller became a newsmaker when DFO would not let reporters talk to her directly. Dr. Miller's genomic research, had correlated survival of the spawning salmon with anti-viral markers in the genome of the sockeye. Further analysis suggested that a parvovirus, first discovered to cause leukemia in farmed chinook salmon was an agent that could possibly explain the changes in gene regulation that she had discovered. This was indeed a significant finding. However, despite what the film may lead you to believe, Dr. Miller did not seem to think that aquaculture farms were the problem. She said it appeared to be occurring in the freshwater environment. The film took a wrong turn in twisting her research and it's implications. There was no evidence presented to suggest that this was first of all coming from farmed Atlantic salmon. Second, the agent wasn't positively identified in the dead Pacific salmon. So, when the film showed an email sent to Dr. Miller, where the emails finished by saying there wasn't any benefit to testing, that was in fact true. They hadn't even confirmed the virus was killing the salmon. If they have no virus, no sequenced virus, then they can't even produce primers to test for it's presence with PCR. More on PCR in a bit.

The next topic presented is the 2009 sockeye returns which initiated the Cohen Commission. For a third year in a row, the Fraser River sockeye were closed to all fishing. Close to 10 million fish that had been estimated to return were gone. Now, it's important to note, that the estimates are modelled, and were only considered to be accurate about 50% of the time. During the Cohen Commission, it was noted that oceanographic and biological conditions had not been optimal. Over the four year period, Dr. Richard Beamish, there had been low abundances in trawl surveys of smolts, high incidences of starved juveniles, extremely high freshwater discharge into the Strit of Georgia, low salinity, high winds, and shallow mixing layers. This contributed to a synchronous failure. During the salmon migration to the marine environment, there are critical thresholds for size and the period. When conditions align, such as poor feeding conditions and harsh environmental effects, this produces a synchronous failure. There is very high mortality in the first six weeks after sea water entry, and Dr. Beamish was explaining that the factors had aligned to make such a case. Dr. Craig Orr at one point in this part of the film is quoted as " [the fish] are not getting the food in the high seas." This is an important factor, and one not often mentioned in these discussions.

I earlier said I would come back to Alaska and aquaculture. One of the dirty secrets of wild salmon, is the number of fish that are called wild, that start their lives in a freshwater hatchery. Some Alaskan runs are now in the majority, originating from the large hatchery system operated by Alaskan government and fisher associations. To put this into context, hatchery production of Pacific salmonids is now approximately 2 billion each year, with Alaska producing about 1.5 billion of that total. To further put that into context, this is more than the combined production of Atlantic salmon smolts for farming in Norway, Chile, the United Kingdom, and Canada combined. There is little doubt that these large numbers of smolts are having an impact on the resources in the Gulf of Alaska.

The film then turns back to viruses. Specifically, the infectious salmon anemia (ISA) controversy. Dr. Rick Routledge supposes that it must be something new which is causing the declining stocks. This is unwarranted supposition. New research has shown that salmon populations vary greatly with time, sometimes on time scales up to 80 years. Therefore modeling of stocks that assume time is not a variable of interest are probably poor predictors, and assuming in the absence of evidence that a declining stock must be evidence of some new threat is specious at best, and at worst an outright attempt to misinform. The ISA controversy began when poor quality samples were sent to a lab at the Atlantic Veterinary College for testing. The OIE reference laboratory run by Dr. Fred Kibenge found two positive results out of 48 fish tested. The analysis used polymerase chain reaction (PCR), a molecular technique which uses snippets of DNA to test for the presence of something. Now, again I will give some more context. The OIE recognizes that PCR, while a powerful molecular tool, can produce erroneous results. Therefore, to confirm a report of this reportable disease, they require corroboration, either with clinical signs of disease, or by growing the agent in cell culture. This was never accomplished with any of the samples Morton and Dr. Routledge sent for analysis. In fact, when Dr. Are Nylund-a world expert on ISA at the other OIE reference laboratory in Norway- tested the same samples, he was only able to get a positive on one sample, and he had to run that sample 33 times to get one positive. That, combined with the failure to produce any cytopathic effects in cell culture, meant that they did not have a positive finding of ISA in BC. When Dr. Nylund was interviewed in Norway, he said as much.For Morton and Routledge though, that was enough to start claiming the virus was found everywhere where salmon are farmed. That is not true. It still to this day has not been confirmed in BC, and salmon are farmed in other areas with no ISA, for instance Australia. Even our trading partners in Oregon, have concluded that based on the evidence it is not found in BC. They also rightly state that the risk is very low, as experiments have been conducted which failed to produce specific mortality.

From here the program begins to be filled with ridiculous conspiracy theories among other ridiculous statements. At one point, Morton compares ISA to mad cow disease. That is flat out ridiculous. Mad cow disease is a result of feeding misfolded proteins, often brain stem material, to cows. ISA is a virus that farmers cannot control by feeding their salmon properly. Further, salmon infected with ISA do not infect humans who eat them. At one point Morton makes an implication that mothers should not be feeding this to their family, for their health. Dr. Routledge follows on with another ridiculous statement which I will paraphrase "Nobody knows what happens when you introduce a virus into a naive population. It might be totally benign, or it might be devastating like small pox". He refers to the arrival of small pox in indigenous populations when North America was being settled. First of all, there is a rather large distinction to be made between population, and species. ISA jumping species is not at all the same as small pox infecting a new population of humans who have never encountered it.Also, as already mentioned above, there is already experimental evidence showing that Pacific salmonids are resistant to ISA, and do not show clinical signs of disease. Later, they delve into conspiracy, by suggesting that the results from CFIA, the audit of Kibenge's lab, are all part of a cover-up by the government to ensure corss border trade. Dr. Routledge even goes so far to say that CFIA is not taking the threat seriously, presumably because they had different results. As mentioned, they could not find any material in cell culture, and nothing to sequence. Going back to the PCR results, a positive test with PCR is not a positive finding of a virus, or bacteria. It is a positive finding for a segment of DNA coded to match the primers used in the polymerization reaction. That is why additional tests are required, and this is why CFIA said they had no positive results. They had none to confirm the results of the PCR tests.

The film takes a disturbing turn when they attempt to smear the name of the provincial veterinarian in BC who performs the pathology and diagnostic testing for the farmed salmon industry. They take Dr. Gary Marty's records out of context by cherry picking the report. For example, in the first report, they highlight the fact that ISA testing was asked for and that mortality had been increasing on the Marine Harvest farm. Well, it is a reportable disease, and farmers want to know if they have ISA. The film accurately described the financial losses the disease can cause, and has caused where it has been found. As for increasing mortality, there are seasonal changes, a background mortality that changes seasonally on each farm. Also noted on the report was the fact that dissolved oxygen had been low on the farm and that there were no lesions associated with those mortalities. Without seeing the report, it's hard to know what else was in there. Low oxygen could be due to an algal bloom, or a seasonal change as a result of warming waters, among other factors.

Heading back to the rivers and the pre-spawn mortality, the film shows many dead fish. At one point they open up a dead fish and say it must have been sick due to all the fluid in the peritoneal cavity. Well ascites is a fluid that can form in sick fish, but dead fish also liquefy. There is no indication of how long the fish had been dead, but it doesn't take long for the bacteria inside a healthy fish that dies, to start putrification. At one point, Morton even identifies the fish as having columnaris, a disease caused by bacteria found all along the west coast, in fact all over the world. Then they show some skinny fish, and conjecture that the fish must have been ill because it is thin. This is nonsense. Some fish are skinny. It's in their genes. Are all skinny humans sick too? Of course not. It's true that a sick fish doesn't eat, but it's not true that a skinny fish must therefore be sick. That is a logical fallacy.

The film closes out, with Morton explaining how she's found piscine reovirus (PRV) and salmonid alphavirus (SAV) in the fish farmed in BC. This again is based only on her PCR testing, not on any cell culture, not on any fully sequenced material. In fact, at one point she shows a picture of two fish hearts. One firm, the other soft. She describes the soft heart as characteristic of heart and skeletal muscle inflammation, a disease that has been associated with PRV. That is true. However, another clinical sign of HSMI is pale hearts. The heart she shows us is dark, almost the colour of beef liver. This is more misdirection, as the soft dark heart is probably due to liquefaction from the putrification of dead tissue.

In the end, the film is highly selective in what they show, relying on cherry picking to remove the larger context of what the full body of scientific literature supports and does not support. The film uses misdirection, even outright falshoods, to slant the viewer towards a conclusion that the farmed salmon industry has brought exotic disease into BC, and that it is the cause of the declining productivity.
Little mention is given to other factors like habitat degradation, pollution, climate change, or even the natural cycles of boom and bust that recent investigations have revealed. The discussion about disease diagnostics is not particularly nuanced, and as a result they skip over some very relevant information in the pathologists handbook when it comes to identifying causes of death. The places in the world where ISA, PRV, and HSMI have been confirmed, have experienced massive economic losses. That simply isn't the case in BC. There have been no farms with 90% death that one could expect in unvaccinated Atlantic salmon. In fact, the biggest threat to farmed salmon in BC is a virus carried naturally by Pacific salmonids, that does not cause clinical disease in Pacific salmonids. It's called Infectious hematopoietic necrosis virus.

All in all, I thought the film was very poor, especially from a scientific stand point. Twyla Roscovich could have done better, by actually talking to the experts in this field, instead of cherry picking quotes that fit the story she set out to tell. And that is what she did. She told a story.